We want to grow an organized structure (a crystal).
The Si wafer is crystalline and can provide a template for this "crystal growth." However, in air, the surface of the wafer oxidizes to grow a thin disordered SiO2 film. To remove this film, the wafer is heated up to 800 Centigrade. At this temperature the oxide evaporates (and in our 10-12 atmosphere, there are few air atoms around to regrow it). The wafer is then cooled to about 550C, just enough heat to allow the arriving Si and Ge atoms to wander across the surface to find a proper crystalline position.
